Small Humanin-Like Peptides (SHLPs) Explained

Humanin and Mitochondrial Peptides

6 Peptides

Six small humanin-like peptides discovered in 2016, each encoded by a distinct open reading frame within the 16S rRNA region of mitochondrial DNA.

Cobb et al., Aging, 2016

Cobb et al., Aging, 2016

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Your mitochondria contain their own genome, a small circular DNA molecule with just 37 genes. For decades, researchers believed this genome encoded only 13 proteins, all components of the electron transport chain. That view changed when humanin was discovered in 2001, the first peptide shown to be encoded by a non-protein-coding region of mitochondrial DNA. Then in 2016, Cobb et al. used computational analysis to identify six more peptides hiding in the same 16S rRNA gene that encodes humanin. They named them small humanin-like peptides: SHLP1 through SHLP6.^[1]

These six peptides range from 20 to 38 amino acids in length. They are part of the growing family of mitochondrial-derived peptides (MDPs), which also includes humanin and MOTS-c. Each SHLP has distinct biological effects. Some protect cells from death. One actively promotes it.

How SHLPs Were Discovered

The discovery of SHLPs followed a straightforward computational logic. Humanin was found encoded within the 16S ribosomal RNA gene of mitochondrial DNA. If one peptide could be encoded by a non-coding region, others might be as well.

Cobb et al. (2016) systematically searched the 16S rRNA gene for additional open reading frames (ORFs) capable of encoding peptides. They identified six, each producing a peptide between 20 and 38 amino acids long.^[1] These ORFs were not annotated in standard mitochondrial genome databases because they fell within a region classified as non-coding. The team confirmed that cells actually produce these peptides by detecting them with targeted antibodies.

The discovery expanded the known output of the mitochondrial genome from 13 proteins plus humanin and MOTS-c to at least 21 gene products. It also challenged the assumption that mitochondrial DNA is fully characterized. If multiple peptides were hiding in a single gene region, the true peptide output of mitochondria may be larger than currently known.

What makes the SHLPs conceptually interesting is that they come from a region classified as ribosomal RNA, not protein-coding sequence. Standard genome annotation would never flag these ORFs. The Cobb et al. approach, scanning for translatable sequences regardless of annotation, suggests that non-coding regions throughout the mitochondrial genome (and possibly the nuclear genome) may harbor additional undiscovered bioactive peptides.

SHLP2: The Protective One

SHLP2 is the most extensively studied member of the family. In the original characterization, Cobb et al. found that SHLP2 treatment reduced apoptosis in cell culture, decreased reactive oxygen species (ROS) generation, and improved mitochondrial oxygen consumption rate, a measure of mitochondrial function.^[1] These protective effects paralleled those of humanin, which is expected given their shared genetic neighborhood.

The insulin sensitization data is particularly striking. In mouse studies, intracerebral infusion of SHLP2 increased whole-body glucose uptake and simultaneously suppressed hepatic glucose production during hyperinsulinemic-euglycemic clamp experiments. This dual action, both peripheral (increased glucose uptake) and central (hypothalamic-mediated suppression of liver glucose output), positions SHLP2 as a potential regulator of metabolic homeostasis. The mechanism appears to involve activation of the Akt signaling pathway, the same cascade that insulin itself triggers.^[2]

Circulating SHLP2 levels decline with age in mice, mirroring the age-related decline in humanin and MOTS-c.^[1] Whether this decline contributes to age-related metabolic dysfunction or is merely correlated with it has not been established.

Sequeira et al. (2021) measured plasma SHLP2 levels in humans without diabetes and found a positive association between SHLP2 and android fat distribution (abdominal fat) and liver fat content.^[3] This finding complicates the simple narrative that SHLP2 is purely protective. If SHLP2 levels track with metabolically unhealthy fat distribution, the peptide's role may be compensatory (rising in response to metabolic stress) rather than purely beneficial. The parallel with insulin is instructive: insulin levels rise in insulin-resistant states as the body tries to compensate, but high insulin is not the cure for insulin resistance. SHLP2 may follow a similar compensatory pattern. The cross-sectional design of the study cannot distinguish between these possibilities, and interventional studies would be required to determine whether SHLP2 elevation is a response to metabolic dysfunction or a contributor to it.

SHLP3: Cytoprotection and Hearing Protection

SHLP3 shares much of SHLP2's protective profile. In the Cobb et al. (2016) characterization, SHLP3 reduced apoptosis and ROS and improved mitochondrial function, essentially recapitulating SHLP2's effects in cell culture.^[1]

A 2024 study by Lu et al. tested SHLP3 in a more specific context: gentamicin-induced damage to cochlear hair cells. Gentamicin is an aminoglycoside antibiotic known to cause irreversible hearing loss by destroying the sensory hair cells in the inner ear. Lu et al. found that both humanin analog HNG and SHLP3 protected these hair cells against gentamicin toxicity.^[4] This is one of the first studies to test any SHLP in a tissue-specific disease model rather than generic cell culture, and it suggests that mitochondrial-derived peptides may have therapeutic relevance in conditions driven by mitochondrial damage in specific cell types.

SHLP4 and SHLP5: Less Studied, Different Effects

SHLP4 promoted cell proliferation in the Cobb et al. characterization without the same anti-apoptotic effects seen with SHLP2 and SHLP3.^[1] Proliferative peptides are a double-edged sword in biology: they could be useful for tissue regeneration but potentially harmful in the context of cancer. No follow-up studies have specifically investigated SHLP4's proliferative mechanism or its behavior in tumor models.

SHLP5 has received almost no independent investigation beyond the original discovery paper. Its biological profile remains poorly characterized. SHLP1 similarly lacks dedicated follow-up studies. Together, SHLP1, SHLP4, and SHLP5 represent the least understood members of the family, each waiting for the kind of focused mechanistic work that has begun to clarify SHLP2's signaling pathways.

SHLP6: The Pro-Apoptotic Outlier

SHLP6 breaks the pattern. While SHLP2 and SHLP3 protect cells from death, SHLP6 actively promotes apoptosis.^[1] This is remarkable because humanin, the defining member of this peptide family, is one of the strongest anti-apoptotic peptides known. SHLP6 appears to do the opposite.

A 2023 study examined evolutionary signatures in mitochondrial-derived peptides and found evidence of natural selection acting on both humanin and SHLP6, suggesting that both peptides serve important biological functions that have been maintained through evolution. The pro-apoptotic function of SHLP6 may serve a quality control role: eliminating damaged or dysfunctional cells that should not survive. Apoptosis is not always pathological. In cancer biology, for instance, restoring apoptosis in tumor cells is a primary therapeutic goal. A mitochondrial peptide that naturally promotes cell death could be relevant to tumor suppression, though this hypothesis has not been directly tested.

The contrast between SHLP2/SHLP3 (anti-apoptotic) and SHLP6 (pro-apoptotic) from the same genetic region raises questions about how mitochondria balance cell survival and cell death signals. One possibility is that relative SHLP ratios, rather than absolute levels, determine the net cellular response. A cell producing high SHLP2 and low SHLP6 would be biased toward survival. A cell producing low SHLP2 and high SHLP6 would be biased toward apoptosis. If mitochondrial stress or damage shifts this ratio, the organelle could effectively vote on whether its host cell should live or die. This hypothesis has not been tested experimentally, but it aligns with the broader concept that mitochondria participate in cell fate decisions through multiple signaling pathways.

SHLPs in the Context of Mitochondrial-Derived Peptides

The MDP family now includes three groups: humanin, MOTS-c, and the six SHLPs. Each emerged from a different region of mitochondrial DNA, and each appears to have distinct signaling pathways.

Humanin acts primarily through FPRL-1 and CXCR4 receptors and has strong anti-apoptotic and neuroprotective effects.^[5] MOTS-c activates AMPK and translocates to the nucleus to regulate gene expression, functioning as a mitochondria-to-nucleus signaling molecule with effects on insulin sensitivity and exercise adaptation.^[6] The SHLPs appear to have partially overlapping but distinct activities, with SHLP2 resembling humanin most closely.

A 2019 review by Popov et al. placed MDPs in the broader therapeutic landscape, noting that mitochondrial peptides represent a new class of signaling molecules that could be exploited for metabolic, cardiovascular, and neurodegenerative diseases.^[7] Li et al. (2024) specifically reviewed MDP cardiovascular applications, noting that SHLP2 and humanin both show cardioprotective effects in preclinical models, potentially through mitochondrial preservation and anti-inflammatory signaling.^[8]

The relationship to other mitochondria-targeting peptides such as SS-31 (elamipretide) is worth noting. SS-31 is a synthetic peptide that targets cardiolipin in the inner mitochondrial membrane, while SHLPs are endogenous peptides encoded by mitochondrial DNA itself. They approach mitochondrial protection from different directions.

What We Do Not Know

The SHLP field is young (the discovery paper was published in 2016) and the evidence base is limited in several ways.

Receptor identification. SHLP2 is known to bind CXCR7, but the receptor targets for SHLP1, SHLP3, SHLP4, SHLP5, and SHLP6 have not been identified. Without receptor binding data, the signaling pathways downstream of most SHLPs remain speculative.

Human data. The Sequeira et al. (2021) study measured circulating SHLP2 in humans, but no interventional human studies have been conducted with any SHLP. All therapeutic claims are based on cell culture or mouse experiments.

Production and regulation. How mitochondria regulate the production of individual SHLPs is unclear. Whether SHLPs are produced constitutively or in response to specific stressors (oxidative stress, metabolic challenge, DNA damage) has not been systematically investigated. The stoichiometry between SHLPs, humanin, and MOTS-c production from the same cell's mitochondria is unknown.

Tissue specificity. Most studies have used generic cell lines (HEK293, neuronal cultures). Whether SHLPs have tissue-specific effects, as the Lu et al. cochlear hair cell study suggests, requires far more investigation across diverse cell types and organs. Mitochondrial content and function vary enormously between tissue types: cardiomyocytes contain thousands of mitochondria per cell, while red blood cells contain none. SHLP production likely varies accordingly, which means the same peptide could have very different biological significance depending on the tissue context.

Senescence paradox. Mendelsohn and Bhatt (2018) noted that some MDPs can exacerbate cellular senescence under certain conditions, adding complexity to the simple narrative of MDPs as uniformly protective molecules.^[9] Whether SHLPs specifically contribute to senescence, or only protect against it, remains unresolved. For the broader context of why mitochondrial decline drives aging, these nuances matter.

The Bottom Line

The six small humanin-like peptides are mitochondrial-encoded molecules discovered in 2016, each with distinct biological effects. SHLP2 and SHLP3 protect cells and improve mitochondrial function. SHLP6 promotes cell death. SHLP2 shows insulin-sensitizing properties in mouse models. The entire field rests on a handful of studies, with no human interventional data, incomplete receptor identification, and critical questions about regulation and tissue specificity that remain unanswered.

Frequently Asked Questions

What are small humanin-like peptides?

Small humanin-like peptides (SHLPs) are six peptides, SHLP1 through SHLP6, encoded by the 16S rRNA gene of mitochondrial DNA. They were discovered in 2016 through computational analysis of the same genetic region that produces humanin (Cobb et al., 2016). They range from 20 to 38 amino acids in length and have diverse biological effects including cytoprotection, insulin sensitization, and apoptosis regulation.

What does SHLP2 do?

SHLP2 reduces apoptosis, decreases reactive oxygen species, and improves mitochondrial oxygen consumption rate in cell culture. In mouse studies, intracerebral SHLP2 infusion increased glucose uptake and suppressed liver glucose production, acting as an insulin sensitizer through Akt pathway activation (Cobb et al., 2016). Circulating SHLP2 levels decline with age.

What is the difference between humanin and SHLPs?

Humanin and SHLPs are all encoded in the 16S rRNA gene of mitochondrial DNA, but they come from different open reading frames within that gene. Humanin is 24 amino acids and is the best-characterized anti-apoptotic mitochondrial peptide. SHLPs have diverse effects: SHLP2 and SHLP3 are cytoprotective (like humanin), SHLP4 promotes proliferation, and SHLP6 is pro-apoptotic (opposite to humanin).

Are SHLPs related to MOTS-c?

SHLPs and MOTS-c are both mitochondrial-derived peptides, but they come from different regions of mitochondrial DNA. SHLPs are encoded in the 16S rRNA gene (MT-RNR2), while MOTS-c is encoded in the 12S rRNA gene (MT-RNR1). MOTS-c primarily activates AMPK and affects exercise response, while SHLP2 primarily works through insulin-Akt signaling and anti-apoptotic pathways.

Do SHLP levels change with age?

Yes. Cobb et al. (2016) found that circulating SHLP2 levels decline with age in mice, following the same pattern seen in humanin and MOTS-c. Whether this decline contributes to age-related disease or is a marker of other aging processes has not been determined. Human data on age-related SHLP decline is limited.

Can SHLPs be used as a treatment?

No SHLP has been tested in a human clinical trial. All therapeutic evidence comes from cell culture and mouse studies. SHLP2 shows promise for metabolic and cytoprotective applications, and SHLP3 protected cochlear hair cells from antibiotic damage in one study (Lu et al., 2024). Translation from these early-stage findings to clinical use remains a distant prospect.